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For: Jing G, Zhang Y, Cui W, Liu L, Xu J, Su X. Meta-Apo improves accuracy of 16S-amplicon-based prediction of microbiome function. BMC Genomics 2021;22:9. [PMID: 33407112 PMCID: PMC7788972 DOI: 10.1186/s12864-020-07307-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Accepted: 12/07/2020] [Indexed: 12/13/2022]  Open
Number Cited by Other Article(s)
1
Matchado MS, Rühlemann M, Reitmeier S, Kacprowski T, Frost F, Haller D, Baumbach J, List M. On the limits of 16S rRNA gene-based metagenome prediction and functional profiling. Microb Genom 2024;10:001203. [PMID: 38421266 PMCID: PMC10926695 DOI: 10.1099/mgen.0.001203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Accepted: 02/05/2024] [Indexed: 03/02/2024]  Open
2
Cerk K, Ugalde‐Salas P, Nedjad CG, Lecomte M, Muller C, Sherman DJ, Hildebrand F, Labarthe S, Frioux C. Community-scale models of microbiomes: Articulating metabolic modelling and metagenome sequencing. Microb Biotechnol 2024;17:e14396. [PMID: 38243750 PMCID: PMC10832553 DOI: 10.1111/1751-7915.14396] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 11/27/2023] [Accepted: 12/20/2023] [Indexed: 01/21/2024]  Open
3
Huang S, Kong Y, Chen Y, Huang X, Ma P, Liu X. Microbial denitrification characteristics of typical decentralized wastewater treatment processes based on 16S rRNA sequencing. Front Microbiol 2023;14:1242506. [PMID: 37779708 PMCID: PMC10537219 DOI: 10.3389/fmicb.2023.1242506] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Accepted: 09/04/2023] [Indexed: 10/03/2023]  Open
4
Zhang W, Fan X, Shi H, Li J, Zhang M, Zhao J, Su X. Comprehensive Assessment of 16S rRNA Gene Amplicon Sequencing for Microbiome Profiling across Multiple Habitats. Microbiol Spectr 2023;11:e0056323. [PMID: 37102867 PMCID: PMC10269731 DOI: 10.1128/spectrum.00563-23] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Accepted: 04/10/2023] [Indexed: 04/28/2023]  Open
5
The association between the respiratory tract microbiome and clinical outcomes in patients with COPD. Microbiol Res 2023;266:127244. [DOI: 10.1016/j.micres.2022.127244] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Revised: 10/25/2022] [Accepted: 10/25/2022] [Indexed: 11/06/2022]
6
Establishment and Validation of a New Analysis Strategy for the Study of Plant Endophytic Microorganisms. Int J Mol Sci 2022;23:ijms232214223. [PMID: 36430699 PMCID: PMC9697482 DOI: 10.3390/ijms232214223] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 11/11/2022] [Accepted: 11/14/2022] [Indexed: 11/19/2022]  Open
7
Trego A, Keating C, Nzeteu C, Graham A, O’Flaherty V, Ijaz UZ. Beyond Basic Diversity Estimates-Analytical Tools for Mechanistic Interpretations of Amplicon Sequencing Data. Microorganisms 2022;10:1961. [PMID: 36296237 PMCID: PMC9609705 DOI: 10.3390/microorganisms10101961] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Revised: 09/29/2022] [Accepted: 09/30/2022] [Indexed: 11/07/2022]  Open
8
Wang J, Qie J, Zhu D, Zhang X, Zhang Q, Xu Y, Wang Y, Mi K, Pei Y, Liu Y, Ji G, Liu X. The landscape in the gut microbiome of long-lived families reveals new insights on longevity and aging - relevant neural and immune function. Gut Microbes 2022;14:2107288. [PMID: 35939616 PMCID: PMC9361766 DOI: 10.1080/19490976.2022.2107288] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]  Open
9
Chen Y, Li J, Zhang Y, Zhang M, Sun Z, Jing G, Huang S, Su X. Parallel-Meta Suite: Interactive and rapid microbiome data analysis on multiple platforms. IMETA 2022;1:e1. [PMID: 38867729 PMCID: PMC10989749 DOI: 10.1002/imt2.1] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 12/13/2021] [Accepted: 12/17/2021] [Indexed: 06/14/2024]
10
Sun Z, Liu X, Jing G, Chen Y, Jiang S, Zhang M, Liu J, Xu J, Su X. Comprehensive understanding to the public health risk of environmental microbes via a microbiome-based index. J Genet Genomics 2022;49:685-688. [PMID: 35017120 DOI: 10.1016/j.jgg.2021.12.011] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 12/20/2021] [Accepted: 12/20/2021] [Indexed: 12/29/2022]
11
Cai Z, Lin S, Hu S, Zhao L. Structure and Function of Oral Microbial Community in Periodontitis Based on Integrated Data. Front Cell Infect Microbiol 2021;11:663756. [PMID: 34222038 PMCID: PMC8248787 DOI: 10.3389/fcimb.2021.663756] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Accepted: 05/31/2021] [Indexed: 02/05/2023]  Open
12
Zhang Y, Jing G, Chen Y, Li J, Su X. Hierarchical Meta-Storms enables comprehensive and rapid comparison of microbiome functional profiles on a large scale using hierarchical dissimilarity metrics and parallel computing. BIOINFORMATICS ADVANCES 2021;1:vbab003. [PMID: 36700101 PMCID: PMC9710644 DOI: 10.1093/bioadv/vbab003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Accepted: 05/06/2021] [Indexed: 01/28/2023]
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